{
  "_id": "6a0f6275acfb0bcc41c5c381",
  "Package": "biomvRCNS",
  "Type": "Package",
  "Title": "Copy Number study and Segmentation for multivariate biological\ndata",
  "Version": "1.53.0",
  "Date": "2021-11-20",
  "Author": "Yang Du",
  "Maintainer": "Yang Du <tooyoung@gmail.com>",
  "Description": "In this package, a Hidden Semi Markov Model (HSMM) and one\nhomogeneous segmentation model are designed and implemented for\nsegmentation genomic data, with the aim of assisting in\ntranscripts detection using high throughput technology like\nRNA-seq or tiling array, and copy number analysis using aCGH or\nsequencing.",
  "License": "GPL (>= 2)",
  "LazyLoad": "yes",
  "biocViews": "aCGH, CopyNumberVariation, Microarray, Sequencing,\nVisualization, Genetics",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:02 UTC",
  "RemoteUrl": "https://github.com/bioc/biomvRCNS",
  "RemoteRef": "HEAD",
  "RemoteSha": "0f85d22a0273c72102963697f620ee71f435a338",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-21 10:37:54 UTC",
    "User": "root"
  },
  "MD5sum": "f52b91239db1cad0eb5f0ae987c23680",
  "_user": "bioc",
  "_type": "src",
  "_file": "biomvRCNS_1.53.0.tar.gz",
  "_fileid": "1b490e0123bda2dd7a8aeb4fbd76141205da778cccefa93c3dbb60f11a0ddcec",
  "_filesize": 726338,
  "_sha256": "1b490e0123bda2dd7a8aeb4fbd76141205da778cccefa93c3dbb60f11a0ddcec",
  "_created": "2026-05-21T10:37:54.000Z",
  "_published": "2026-05-21T19:52:21.951Z",
  "_jobs": [
    {
      "job": 77255877884,
      "time": 260,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7133626889"
    },
    {
      "job": 77255878168,
      "time": 419,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7133678734"
    },
    {
      "job": 77255877569,
      "time": 499,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7133704394"
    },
    {
      "job": 77255878013,
      "time": 416,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7133678081"
    },
    {
      "job": 77255878344,
      "time": 481,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7133698701"
    },
    {
      "job": 77255878208,
      "time": 579,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7133729823"
    },
    {
      "job": 77255877953,
      "time": 665,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7133757706"
    },
    {
      "job": 77255877618,
      "time": 326,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7133648976"
    },
    {
      "job": 77255877772,
      "time": 675,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7133760734"
    },
    {
      "job": 77255877387,
      "time": 370,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7133543767"
    },
    {
      "job": 77255877048,
      "time": 204,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7145730198"
    },
    {
      "job": 77255877949,
      "time": 379,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7133666011"
    },
    {
      "job": 77255877808,
      "time": 416,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7133677934"
    },
    {
      "job": 77255877663,
      "time": 458,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7133692693"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 6,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/biomvRCNS",
  "_commit": {
    "id": "0f85d22a0273c72102963697f620ee71f435a338",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381322
  },
  "_maintainer": {
    "name": "Yang Du",
    "email": "tooyoung@gmail.com"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "Gviz",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "dynamicTreeCut",
      "role": "Suggests"
    },
    {
      "package": "Rsamtools",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.53.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.52.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "acgh",
    "copynumbervariation",
    "microarray",
    "sequencing",
    "visualization",
    "genetics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 480,
    "source": "https://www.bioconductor.org/packages/stats/bioc/biomvRCNS"
  },
  "_mentions": 1,
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/biomvRCNS.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "biomvRGviz",
    "biomvRhsmm",
    "biomvRmgmr",
    "biomvRseg",
    "hsmmRun",
    "maxGapminRun",
    "regionSegAlphaNB",
    "regionSegCost",
    "show",
    "simSegData",
    "sojournAnno",
    "splitFarNeighbour"
  ],
  "_datasets": [
    {
      "name": "coriell",
      "title": "Array CGH data set of Coriell cell lines",
      "object": "coriell",
      "file": "coriell.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Clone",
        "Chromosome",
        "Position",
        "Coriell.05296",
        "Coriell.13330"
      ],
      "rows": 2271,
      "table": true,
      "tojson": true
    },
    {
      "name": "encodeTP53",
      "title": "mapped RNA-seq data from ENCODE",
      "object": "encodeTP53",
      "file": "encodeTP53.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "variosm",
      "title": "Differential methylation data from sequencing",
      "object": "variosm",
      "file": "variosm.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "biomvRCNS-class",
      "title": "Class '\"biomvRCNS\"'",
      "topics": [
        "biomvRCNS-class",
        "plot,biomvRCNS,ANY-method",
        "show,biomvRCNS-method"
      ]
    },
    {
      "page": "biomvRGviz",
      "title": "Plot segmentation result using Gviz",
      "topics": [
        "biomvRGviz"
      ]
    },
    {
      "page": "biomvRhsmm",
      "title": "Estimating the most likely state sequence using Hidden Semi Markov Model",
      "topics": [
        "biomvRhsmm"
      ]
    },
    {
      "page": "biomvRmgmr",
      "title": "Batch process multiple sequences and samples using max-gap-min-run algorithm for 2 states segmentation",
      "topics": [
        "biomvRmgmr"
      ]
    },
    {
      "page": "biomvRseg",
      "title": "Homogeneous segmentation of multi-sample genomic data",
      "topics": [
        "biomvRseg"
      ]
    },
    {
      "page": "coriell",
      "title": "Array CGH data set of Coriell cell lines",
      "topics": [
        "coriell"
      ]
    },
    {
      "page": "encodeTP53",
      "title": "mapped RNA-seq data from ENCODE",
      "topics": [
        "encodeTP53"
      ]
    },
    {
      "page": "hsmmRun",
      "title": "Estimating the most likely state sequence using Hidden Semi Markov Model",
      "topics": [
        "hsmmRun"
      ]
    },
    {
      "page": "maxGapminRun",
      "title": "Max-gap-min-run algorithm for 2 states segmentation",
      "topics": [
        "maxGapminRun"
      ]
    },
    {
      "page": "regionSegAlphaNB",
      "title": "Estimate matrix of dispersion parameter alpha (size) used in 'regionSegCost' for negative binomial distributed 'x'.",
      "topics": [
        "regionSegAlphaNB"
      ]
    },
    {
      "page": "regionSegCost",
      "title": "Regional segmentation cost matrix",
      "topics": [
        "regionSegCost"
      ]
    },
    {
      "page": "simSegData",
      "title": "Simulate exemplary segmentation data.",
      "topics": [
        "simSegData"
      ]
    },
    {
      "page": "sojournAnno",
      "title": "Estimate sojourn distribution parameters from posterior information like annotation data",
      "topics": [
        "sojournAnno"
      ]
    },
    {
      "page": "splitFarNeighbour",
      "title": "Split segments if long gaps exist between feature positions",
      "topics": [
        "splitFarNeighbour"
      ]
    },
    {
      "page": "variosm",
      "title": "Differential methylation data from sequencing",
      "topics": [
        "variosm"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "checkmate",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "dichromat",
    "digest",
    "dplyr",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "Gviz",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "mvtnorm",
    "nnet",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "biomvRCNS.Rnw",
      "filename": "biomvRCNS.pdf",
      "title": "biomvRCNS package introduction",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-10-20 07:36:26",
      "modified": "2016-02-22 10:40:25",
      "commits": 6
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "biomvrcns",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-05-21T10:42:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "be066ffe352691177e55b2421fd3476d1c775ef33c21263032c0ca0a6786f3bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-05-21T10:42:13.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "4f0b334b3c4c82e80c287f70bbc81992f2b2c68d42280ab0c85f69b171eb12c4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-05-21T10:41:53.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "182697fd2f6e54ba495a0aef8acaa5f70595b8a011067a06be1d9d589af4227b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-05-21T10:42:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "9945a020e28768c5ff32f6a5118a0e7156dbe221f1a136d4bbb14656e2e9d098",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-05-21T10:43:36.000Z",
      "arch": "aarch64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "c738e9dee30cb449d31c18eeac45ebee8776a05b002d6eb7f31f1b266b70a658",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-05-21T10:44:50.000Z",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "b3238925a1ecf8edc7d2bc40daa0a7a8691b39ba63792171a430f8de0bb04dfe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-05-21T10:40:56.000Z",
      "arch": "aarch64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "e6f678d23d7da47ed1241c47f4d63923fa2166263fb277231e333dee8aad1bec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-05-21T10:44:59.000Z",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "666fa96d550e77803ff6213e1d1be5f96798f4be2282ab7580bf52c8c69c8e99",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.53.0",
      "date": "2026-05-21T19:51:53.000Z",
      "arch": "emscripten",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "b5fa41fde834d61b41a9bba7cd30940782ec5bcda437e3f1e1a69d3ca02b9b1e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.53.0",
      "date": "2026-05-21T10:40:43.000Z",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "ea167487a8a48960ef4795ab858d80c16cf44269957cc671a54882d4817c6133",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.53.0",
      "date": "2026-05-21T10:40:39.000Z",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "45fb3f05ab28f8f825cc241e31cafa88df680484991ce0db5e42f1913fe6320d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.53.0",
      "date": "2026-05-21T10:41:49.000Z",
      "arch": "x86_64",
      "commit": "0f85d22a0273c72102963697f620ee71f435a338",
      "fileid": "b0fe75f91c72fdf13feb325444b2c41a0c2b909ba65f1b61ecd2e56c71359d37",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220626455"
    }
  ]
}